Zhongmin Dai

Geographic patterns of co-occurrence network topological features for soil microbiota at continental scale in eastern China

Soil microbiota play a critical role in soil biogeochemical processes and have a profound effect on soil functions. Recent studies have revealed microbial co-occurrence patterns in soil microbial communities, yet the geographic pattern of topological features in soil microbial co-occurrence networks at the continental scale are largely unknown. Here, we investigated the shifts of topological features in co-occurrence networks inferred from soil microbiota along a continental scale in eastern China. Integrating archaeal, bacterial and fungal community datasets, we inferred a meta-community co-occurrence network and analyzed node-level and network-level topological shifts associated with five climatic regions. Both node-level and network-level topological features revealed geographic patterns wherein microorganisms in the northern regions had closer relationships but had a lower interaction influence than those in the southern regions. We further identified topological differences associated with taxonomic groups and demonstrated that co-occurrence patterns were random for archaea and non-random for bacteria and fungi. Given that microbial interactions may contribute to soil functions more than species diversity, this geographic shift of topological features provides new insight into studying microbial biogeographic patterns, their organization and impacts on soil-associated function.

Potential role of biochars in decreasing soil acidification - A critical review

A large number of soils, worldwide, are acid (normally pH<5.5) and suffering from on-going soil acidification. Acid soils or soils undergoing acidification generally have low fertility and low crop productivity. Biochars have been reported to be of potential value in agriculture for improving soil properties and in reducing the hazards caused by soil acidification and in naturally acidic soils. However, the ameliorant effects of biochars on acid soils and the mechanisms involved have not previously been critically reviewed. Here we summarize the phenomena, and mechanisms involved in the improvement of soil acidity by biochars, the alleviation of aluminum toxicity, the enhancement of nutrient availability, and changes in nitrification by collating data in the literature. In addition, the agronomic effectiveness and environmental concerns in the incorporation of biochar and other soil additives (i.e. lime, industrial by-products, organic wastes and plant residues) to acid soils are systemically compared. We conclude that biochar is a potentially effective amendment to reverse or to prevent acidification in acid soils. Finally, perspectives for further research in terms of soil acidification are presented to address some issues that are still poorly understood and/or highly controversial.

Increased Agronomic and Environmental Value Provided by Biochars with Varied Physiochemical Properties Derived from Swine Manure Blended with Rice Straw

To compensate for the shortcomings of manure biochar, an lignocellulose-based feedstock (rice straw) was added into manure-based feedstock (swine manure) at 3:1, 1:1, and 1:3 (w/w) manure/straw ratios during biochar production within the pyrolysis temperature ranging from 300 to 700 °C. The results showed that the pyrolysis temperatures and the proportions of straw added both influenced the biochar properties. The overall properties of biochars at 300, 400, and 500 °C were thoroughly different from those at 600 and 700 °C by principal components analysis (PCA). The XRD, FTIR, and SEM spectra suggested that the addition of straw considerably changed the mineral crystals, functional groups, and porous structures in manure biochar, respectively. The Zn(II) adsorption batch experiments showed that the biochars with more proportions of manure had the largest Zn(II) adsorption capacity than other biochars at 300 °C, which was attributed to the mineral components, oxygen functional groups, and surface areas. To meet varied agronomic and environmental requirements, the different conditions including pyrolysis temperatures and proportions of straw added should be quantitated.

Distinct biogeographic patterns for archaea, bacteria, and fungi along the vegetation gradient at the continental scale in Eastern China

Understanding biogeographic patterns is a precursor to improving our knowledge of the function of microbiomes and to predicting ecosystem responses to environmental change. Using natural forest soil samples from 110 locations, this study is one of the largest attempts to comprehensively understand the different patterns of soil archaeal, bacterial, and fungal biogeography at the continental scale in eastern China. These patterns in natural forest sites could ascertain reliable soil microbial biogeographic patterns by eliminating anthropogenic influences. This information provides guidelines for monitoring the belowground ecosystem’s decline and restoration. Meanwhile, the deviations in the soil microbial communities from corresponding natural forest states indicate the extent of degradation of the soil ecosystem. Moreover, given the association between vegetation type and the microbial community, this information could be used to predict the long-term response of the underground ecosystem to the vegetation distribution caused by global climate change. ABSTRACT The natural forest ecosystem in Eastern China, from tropical forest to boreal forest, has declined due to cropland development during the last 300 years, yet little is known about the historical biogeographic patterns and driving processes for the major domains of microorganisms along this continental-scale natural vegetation gradient. We predicted the biogeographic patterns of soil archaeal, bacterial, and fungal communities across 110 natural forest sites along a transect across four vegetation zones in Eastern China. The distance decay relationships demonstrated the distinct biogeographic patterns of archaeal, bacterial, and fungal communities. While historical processes mainly influenced bacterial community variations, spatially autocorrelated environmental variables mainly influenced the fungal community. Archaea did not display a distance decay pattern along the vegetation gradient. Bacterial community diversity and structure were correlated with the ratio of acid oxalate-soluble Fe to free Fe oxides (Feo/Fed ratio). Fungal community diversity and structure were influenced by dissolved organic carbon (DOC) and free aluminum (Ald), respectively. The role of these environmental variables was confirmed by the correlations between dominant operational taxonomic units (OTUs) and edaphic variables. However, most of the dominant OTUs were not correlated with the major driving variables for the entire communities. These results demonstrate that soil archaea, bacteria, and fungi have different biogeographic patterns and driving processes along this continental-scale natural vegetation gradient, implying different community assembly mechanisms and ecological functions for archaea, bacteria, and fungi in soil ecosystems. IMPORTANCE Understanding biogeographic patterns is a precursor to improving our knowledge of the function of microbiomes and to predicting ecosystem responses to environmental change. Using natural forest soil samples from 110 locations, this study is one of the largest attempts to comprehensively understand the different patterns of soil archaeal, bacterial, and fungal biogeography at the continental scale in eastern China. These patterns in natural forest sites could ascertain reliable soil microbial biogeographic patterns by eliminating anthropogenic influences. This information provides guidelines for monitoring the belowground ecosystem’s decline and restoration. Meanwhile, the deviations in the soil microbial communities from corresponding natural forest states indicate the extent of degradation of the soil ecosystem. Moreover, given the association between vegetation type and the microbial community, this information could be used to predict the long-term response of the underground ecosystem to the vegetation distribution caused by global climate change. Author Video: An author video summary of this article is available.

Sensitive responders among bacterial and fungal microbiome to pyrogenic organic matter (biochar) addition differed greatly between rhizosphere and bulk soils

Sensitive responses among bacterial and fungal communities to pyrogenic organic matter (PyOM) (biochar) addition in rhizosphere and bulk soils are poorly understood. We conducted a pot experiment with manure and straw PyOMs added to an acidic paddy soil, and identified the sensitive “responders” whose relative abundance was significantly increased/decreased among the whole microbial community following PyOM addition. Results showed that PyOMs significantly (p < 0.05) increased root growth, and simultaneously changed soil chemical parameters by decreasing soil acidity and increasing biogenic resource. PyOM-induced acidity and biogenic resource co-determined bacterial responder community structure whereas biogenic resource was the dominant parameter structuring fungal responder community. Both number and proportion of responders in rhizosphere soil was larger than in bulk soil, regardless of PyOM types and microbial domains, indicating the microbial community in rhizosphere soil was sensitive to PyOM addition than bulk soil. The significant increased root biomass and length caused by PyOM addition, associated with physiological processes, e.g. C exudates secretion, likely favored more sensitive responders in rhizosphere soil than in bulk soil. Our study identified the responders at fine taxonomic resolution in PyOM amended soils, improved the understanding of their ecological phenomena associated with PyOM addition, and examined their interactions with plant roots.

Bacterial Community Composition Associated with Pyrogenic Organic Matter (Biochar) Varies with Pyrolysis Temperature and Colonization Environment

Pyrogenic organic matter (PyOM) is widely distributed in soil and fluvial ecosystems and plays an important role in biogeochemical cycling. Many studies have reported changes in soil microbial communities stimulated by PyOM, but very little is known about the microbial communities associated with PyOM. The microbes that colonize PyOMs can participate in the mineralization of PyOM, so changing its structure affects the fate of PyOMs and contributes to soil biogeochemical cycling. This study identified the bacterial community composition associated with PyOMs on the basis of high-throughput sequencing and demonstrated that both PyOM pyrolysis temperature and the colonization environment determined the bacterial community composition. Our work increases our understanding of the dominant phylogenetic taxa associated with PyOMs, demonstrates mechanisms mediating microbial metabolism and growth in PyOMs, and expands a new research area for pyrogenic organic matter. This study identified the bacterial community composition associated with PyOM, which is widely distributed in the environment. Most bacterial OTUs preferentially thrived on PyOM pyrolyzed at low temperature, while some specific OTUs thrived on PyOM pyrolyzed at high temperature. ABSTRACT Microbes that colonize pyrogenic organic matter (PyOM) (also called biochar) play an important role in PyOM mineralization and crucially affect soil biogeochemical cycling, while the microbial community composition associated with PyOM particles is poorly understood. We generated two manure-based PyOMs with different characteristics (PyOM pyrolyzed at the low temperature of 300°C [i.e., PyOM300] and at the high temperature of 700°C [i.e., PyOM700]) and added them to high-carbon (4.15%) and low-C (0.37%) soil for microbial colonization. 16S rRNA gene sequencing showed that Actinobacteria, particularly Actinomycetales, was the dominant taxon in PyOM, regardless of the PyOM pyrolysis temperature and soil type. Bacterial communities associated with PyOM particles from high-C soils were similar to those in non-PyOM-amended soils. PyOM300 had higher total microbial activity and more differential bacterial communities than PyOM700. More bacterial operational taxonomic units (OTUs) preferentially thrived on the low-pyrolysis-temperature PyOM, while some specific OTUs thrived on high-pyrolysis-temperature PyOM. In particular, Chloroflexi species tended to be more prevalent in high-pyrolysis-temperature PyOM in low-C soils. In conclusion, the differences in colonized bacterial community composition between the different PyOMs were strongly influenced by the pyrolysis temperatures of PyOM, i.e., under conditions of easily mineralizable C or fused aromatic C, and by other properties, e.g., pH, surface area, and nutrient content. IMPORTANCE Pyrogenic organic matter (PyOM) is widely distributed in soil and fluvial ecosystems and plays an important role in biogeochemical cycling. Many studies have reported changes in soil microbial communities stimulated by PyOM, but very little is known about the microbial communities associated with PyOM. The microbes that colonize PyOMs can participate in the mineralization of PyOM, so changing its structure affects the fate of PyOMs and contributes to soil biogeochemical cycling. This study identified the bacterial community composition associated with PyOMs on the basis of high-throughput sequencing and demonstrated that both PyOM pyrolysis temperature and the colonization environment determined the bacterial community composition. Our work increases our understanding of the dominant phylogenetic taxa associated with PyOMs, demonstrates mechanisms mediating microbial metabolism and growth in PyOMs, and expands a new research area for pyrogenic organic matter. This study identified the bacterial community composition associated with PyOM, which is widely distributed in the environment. Most bacterial OTUs preferentially thrived on PyOM pyrolyzed at low temperature, while some specific OTUs thrived on PyOM pyrolyzed at high temperature.

Long‐term nitrogen fertilization decreases bacterial diversity and favors the growth of Actinobacteria and Proteobacteria in agro‐ecosystems across the globe

Long-term elevated nitrogen (N) input from anthropogenic sources may cause soil acidification and decrease crop yield, yet the response of the belowground microbial community to long-term N input alone or in combination with phosphorus (P) and potassium (K) is poorly understood. We explored the effect of long-term N and NPK fertilization on soil bacterial diversity and community composition using meta-analysis of a global dataset. Nitrogen fertilization decreased soil pH, and increased soil organic carbon (C) and available N contents. Bacterial taxonomic diversity was decreased by N fertilization alone, but was increased by NPK fertilization. The effect of N fertilization on bacterial diversity varied with soil texture and water management, but was independent of crop type or N application rate. Changes in bacterial diversity were positively related to both soil pH and organic C content under N fertilization alone, but only to soil organic C under NPK fertilization. Microbial biomass C decreased with decreasing bacterial diversity under long-term N fertilization. Nitrogen fertilization increased the relative abundance of Proteobacteria and Actinobacteria, but reduced the abundance of Acidobacteria, consistent with the general life history strategy theory for bacteria. The positive correlation between N application rate and the relative abundance of Actinobacteria indicates that increased N availability favored the growth of Actinobacteria. This first global analysis of long-term N and NPK fertilization that differentially affects bacterial diversity and community composition provides a reference for nutrient management strategies for maintaining belowground microbial diversity in agro-ecosystems worldwide.

Impact of Pyrolysis Time and Temperature on Physicochemical Characteristics of Biochars from Wetland Plants

In this study, two wetland plants (Ravenna grass and Thalia dealbata) were pyrolyzed at 300°C and 500°C for 2 h and 4 h in muffle furnace for biochar production, respectively, and their physical and chemical properties were investigated. Results revealed that the ash content, pH, C, N, CEC, EC, and P in biochars at 500°C were higher than at 300°C, while the yield, O, and H in biochars were opposite. The content of K, Mg, and Na in all types of wetland plant biochars was also higher at 500°C than at 300°C, but Mg content was not the case. However, no significant effect of pyrolysis time at both temperatures was observed in the physiochemical properties of various biochars.

Genetic correlation network prediction of forest soil microbial functional organization

Soil ecological functions are largely determined by the activities of soil microorganisms, which, in turn, are regulated by relevant interactions between genes and their corresponding pathways. Therefore, the genetic network can theoretically elucidate the functional organization that supports complex microbial community functions, although this has not been previously attempted. We generated a genetic correlation network based on 5421 genes derived from metagenomes of forest soils, identifying 7191 positive and 123 negative correlation relationships. This network consisted of 27 clusters enriched with sets of genes within specific functions, represented with corresponding cluster hubs. The clusters revealed a hierarchical architecture, reflecting the functional organization in the soil metagenomes. Positive correlations mapped functional associations, whereas negative correlations often mapped regulatory processes. The potential functions of uncharacterized genes were predicted based on the functions of located clusters. The global genetic correlation network highlights the functional organization in soil metagenomes and provides a resource for predicting gene functions. We anticipate that the genetic correlation network may be exploited to comprehensively decipher soil microbial community functions.